Challenge 09: Skills, knowledge, and technology for all

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Ocean Decade

Challenge 09:
Skills, knowledge, and technology for all

Ensure comprehensive capacity development and equitable access to data, information, knowledge and technology across all aspects of ocean science and for all stakeholders.

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Detection of horizontal gene transfer in the genome of the choanoflagellate Salpingoeca rosetta
Matriano, Danielle M.; Alegado, Rosanna A.; Conaco, Cecilia (Springer, 2021-03-16)
Horizontal gene transfer (HGT), the movement of heritable materials between distantly related organisms, is crucial in eukaryotic evolution. However, the scale of HGT in choanoflagellates, the closest unicellular relatives of metazoans, and its possible roles in the evolution of animal multicellularity remains unexplored. We identified at least 175 candidate HGTs in the genome of the colonial choanoflagellate Salpingoeca rosetta using sequence-based tests. The majority of these were orthologous to genes in bacterial and microalgal lineages, yet displayed genomic features consistent with the rest of the S. rosetta genome—evidence of ancient acquisition events. Putative functions include enzymes involved in amino acid and carbohydrate metabolism, cell signaling, and the synthesis of extracellular matrix components. Functions of candidate HGTs may have contributed to the ability of choanoflagellates to assimilate novel metabolites, thereby supporting adaptation, survival in diverse ecological niches, and response to external cues that are possibly critical in the evolution of multicellularity in choanoflagellates.
We thank Joshua Dizon and Francis Tablizo of the Philippine Genome Center Core Facility for Bioinformatics for assistance with scripts and database construction. We thank Becca Lensing (University of Hawai’i), Cheryl Andam (University of New Hampshire), Deo Onda and Ron Leonard Dy (University of the Philippines) for insightful comments and suggestions on the analysis and interpretation of the data. This work was supported by thesis grants from the Department of Science and Technology Accelerated Science and Technology Human Resource Development Program-National Science Consortium (DOST-ASTHRDP-NSC) and the University of the Philippines Marine Science Institute to DM.
Spatial planning insights for Philippine coral reef conservation using larval connectivity networks
Pata, Patrick R.; Yñiguez, Aletta T. (Frontiers Media SA, 2021-10-06)
The marine habitats of the Philippines are recognized to be some of the most biodiverse systems globally yet only 1.7% of its seas are designated as marine protected areas (MPAs) with varying levels of implementation. Many of these MPAs were established based on local-scale conservation and fisheries objectives without considering larger-scale ecological connections. The connectivity of reefs through larval dispersal is important in the regional-scale resilience against anthropogenic disturbances and is considered a significant criterion in planning for MPAs. In this study, we provide insights into the delineation of ecologically connected MPA networks using larval dispersal modeling and network analysis. We characterized the network properties of the Philippine coral reefs, organized as 252 reef nodes, based on the larval connectivity networks of a branching coral, sea urchin, and grouper. We then evaluated the distribution of the existing 1,060 MPAs relative to the connectivity patterns. All reef nodes were found to be highly interconnected with a mean shortest path ranging from 1.96 to 4.06. Reef nodes were then ranked according to their relative importance in regional connectivity based on five connectivity indices. Despite the between-organism and between-index variability in rankings, there were reefs nodes, mostly located offshore and at major straits, which consistently ranked high. We found that the distribution of existing MPAs partially capture some of the regional connectivity functions but there is a spatial mismatch between the primarily coastal MPAs and the high-ranking reef nodes. Furthermore, network partitioning identified subnetworks and dispersal barriers. The existing MPAs were found to be disproportionately distributed to a few subnetworks and that the largest subnetworks do not contain the greatest number of MPAs. Considering these gaps, we suggest expanding the coverage of protected areas especially in underrepresented reef networks to meaningfully capture national-scale connectivity and meet global conservation objectives.
We would like to thank Dr. Vera Horigue and Andrew Torres for constructive comments and suggestions during the early versions of this paper. We also thank the members of the Biological Oceanography and Modeling of Ecosystems (BiOME) Laboratory who assisted in running model simulations.
Modified oxylipins as inhibitors of biofilm formation in Staphylococcus epidermidis
Peran, Jacquelyn E.; Salvador-Reyes, Lilibeth A. (Frontiers Media SA, 2024-05-23)
New approaches to combating microbial drug resistance are being sought, with the discovery of biofilm inhibitors considered as alternative arsenal for treating infections. Natural products have been at the forefront of antimicrobial discovery and serve as inspiration for the design of new antibiotics. We probed the potency, selectivity, and mechanism of anti-biofilm activity of modified oxylipins inspired by the marine natural product turneroic acid. Structure-activity relationship (SAR) evaluation revealed the importance of the trans-epoxide moiety, regardless of the position, for inhibiting biofilm formation. trans-12,13-epoxyoctadecanoic acid (1) and trans-9,10 epoxyoctadecanoic acid (4) selectively target the early stage of biofilm formation, with no effect on planktonic cells. These compounds interrupt the formation of a protective polysaccharide barrier by significantly upregulating the ica operon’s transcriptional repressor. This was corroborated by docking experiment with SarA and scanning electron micrographs showing reduced biofilm aggregates and the absence of thread-like structures of extrapolymeric substances. In silico evaluation revealed that 1 and 4 can interfere with the AgrA-mediated communication language in Staphylococci, typical to the diffusible signal factor (DSF) capacity of lipophilic chains.
Mining small molecules from Teredinibacter turnerae strains isolated from Philippine Teredinidae
Villacorta, Jamaine B.; Rodriguez, Camille V.; Peran, Jacquelyn E.; Batucan, Jeremiah D.; Concepcion, Gisela; Salvador-Reyes, Lilibeth A.; Junio, Hiyas A. (MDPI, 2022-11-21)
Endosymbiotic relationship has played a significant role in the evolution of marine species, allowing for the development of biochemical machinery for the synthesis of diverse metabolites. In this work, we explore the chemical space of exogenous compounds from shipworm endosymbionts using LC-MS-based metabolomics. Priority T. turnerae strains (1022X.S.1B.7A, 991H.S.0A.06B, 1675L.S.0A.01) that displayed antimicrobial activity, isolated from shipworms collected from several sites in the Philippines were cultured, and fractionated extracts were subjected for profiling using ultrahigh-performance liquid chromatography with high-resolution mass spectrometry quadrupole time-of-flight mass analyzer (UHPLC-HRMS QTOF). T. turnerae T7901 was used as a reference microorganism for dereplication analysis. Tandem MS data were analyzed through the Global Natural Products Social (GNPS) molecular networking, which resulted to 93 clusters with more than two nodes, leading to four putatively annotated clusters: lipids, lysophosphatidylethanolamines, cyclic dipeptides, and rhamnolipids. Additional clusters were also annotated through molecular networking with cross-reference to previous publications. Tartrolon D cluster with analogues, turnercyclamycins A and B; teredinibactin A, dechloroteredinibactin, and two other possible teredinibactin analogues; and oxylipin (E)-11-oxooctadec-12-enoic acid were putatively identified as described. Molecular networking also revealed two additional metabolite clusters, annotated as lyso-ornithine lipids and polyethers. Manual fragmentation analysis corroborated the putative identification generated from GNPS. However, some of the clusters remained unclassified due to the limited structural information on marine natural products in the public database. The result of this study, nonetheless, showed the diversity in the chemical space occupied by shipworm endosymbionts. This study also affirms the use of bioinformatics, molecular networking, and fragmentation mechanisms analysis as tools for the dereplication of high-throughput data to aid the prioritization of strains for further analysis.
The research was completed under the supervision of the Department of Agriculture-Bureau of Fisheries and Aquatic Resources (DA-BFAR), Philippines in compliance with Prior Informed Consent (PIC) certificate requirements and all required legal instruments and regulatory issuances covering the conduct of the research. The authors would also like to acknowledge the Department of Science and Technology-funded Discovery and Development of Health Products Program (DOST-DDHP) for the LC-MS Facility of the Institute of Chemistry, University of the Philippines Diliman.
Decadal stability in coral cover could mask hidden changes on reefs in the East Asian Seas
Chan, Y. K. S.; Affendi, Y. A.; Ang, P. O.; Baria-Rodriguez, M. V.; Chen, C. A.; Chui, A. P. Y.; Glue, M.; Huang, H.; Kuo, C-Y.; Kim, S. W.; Lam, V. Y. Y.; Lane, D. J. W.; Lian, J. S.; Lin, S. M. N. N.; Lunn, Z.; Nañola, C. L.; Nguyen, V. L.; Park, H. S.; Sutthacheep, M.; Vo, S. T.; Vibol, O.; Waheed, Z.; Yamano, H.; Yeemin, T.; Yong, E.; Kimura, T.; Tun, K.; Chou, L. M.; Huang, D. (Springer, 2023-06-10)
Coral reefs in the Central Indo-Pacific region comprise some of the most diverse and yet threatened marine habitats. While reef monitoring has grown throughout the region in recent years, studies of coral reef benthic cover remain limited in spatial and temporal scales. Here, we analysed 24,365 reef surveys performed over 37 years at 1972 sites throughout East Asia by the Global Coral Reef Monitoring Network using Bayesian approaches. Our results show that overall coral cover at surveyed reefs has not declined as suggested in previous studies and compared to reef regions like the Caribbean. Concurrently, macroalgal cover has not increased, with no indications of phase shifts from coral to macroalgal dominance on reefs. Yet, models incorporating socio-economic and environmental variables reveal negative associations of coral cover with coastal urbanisation and sea surface temperature. The diversity of reef assemblages may have mitigated cover declines thus far, but climate change could threaten reef resilience. We recommend prioritisation of regionally coordinated, locally collaborative long-term studies for better contextualisation of monitoring data and analyses, which are essential for achieving reef conservation goals.
Sea surface carbonate dynamics at reefs of Bolinao, Philippines: Seasonal variation and fish mariculture-induced forcing
Isah, Raffi R.; Enochs, Ian C.; San Diego-McGlone, Maria Lourdes (Frontiers, 2022-11-11)
Coral reefs are vulnerable to global ocean acidification (OA) and local human activities will continue to exacerbate coastal OA. In Bolinao, Philippines, intense unregulated fish mariculture has resulted in regional eutrophication. In order to examine the coastal acidification associated with this activity and the impact on nearby coral reefs, water quality and carbonate chemistry parameters were measured at three reef sites, a mariculture site and an offshore, minimally impacted control site during both the wet and dry season. Additionally, benthic community composition was characterized at reef sites, and both autonomous carbonate chemistry sampling and high-frequency pH measurements were used to characterize fine-scale (diel) temporal variability. Water quality was found to be poorer at all reefs during the wet season, when there was stronger outflow of waters from the mariculture area. Carbonate chemistry parameters differed significantly across the reef flat and between seasons, with more acidic conditions occurring during the dry season and increased primary production suppressing further acidification during the wet season. Significant relationships of both total alkalinity (TA) and dissolved inorganic carbon (DIC) with salinity across all stations may imply outflow of acidified water originating from the mariculture area where pH values as low as 7.78 were measured. This apparent mariculture-induced coastal acidification was likely due to organic matter respiration as sustained mariculture will continue to deliver organic matter. While TA-DIC vector diagrams indicate greater contribution of net primary production, net calcification potential in the nearest reef to mariculture area may already be diminished. The two farther reefs, characterized by higher coral cover, indicates healthier ecosystem functioning. Here we show that unregulated fish mariculture activities can lead to localized acidification and impact reef health. As these conditions at times approximate those projected to occur globally due to OA, our results may provide insight into reef persistence potential worldwide. These results also underscore the importance of coastal acidification and indicate that actions taken to mitigate OA on coral reefs should address not only global CO2 emissions but also local perturbations, in this case fish mariculture-induced eutrophication.
This paper is part of the master’s thesis of RI supervised by MS-M entitled “Carbonate chemistry dynamics on the Bolinao reef flat”. The authors are grateful to the Marine Biogeochemistry Laboratory and Bolinao Marine Laboratory of the Marine Science Institute, University of the Philippines for the valuable logistical and laboratory support provided. We thank Jay Burce, Ryan Carl Magyaya, Natasha Tamayo for their tremendous help in field activities and laboratory analyses. We thank Alice Webb for providing insights into improving the manuscript.
Trans-Arctic asymmetries, melting pots and weak species cohesion in the low-dispersal amphiboreal seaweed Fucus distichus
Neiva, João; Assis, Jorge; Fragkopoulou, Eliza; Pearson, Gareth A.; Raimondi, Peter T.; Anderson, Laura; Krause-Jensen, Dorte; Marbà, Núria; Want, Andrew; Selivanova, Olga; Nakaoka, Masahiro; Grant, W. Stewart; Konar, Brenda; Roleda, Michael Y.; Sejr, Mikael K.; Paulino, Cristina; Serrão, Ester A. (Frontiers Media SA, 2024-04-18)
Amphiboreal taxa are often composed of vicariant phylogroups and species complexes whose divergence and phylogeographic affinities reflect a shared history of chronic isolation and episodic trans-Arctic dispersal. Ecological filters and shifting selective pressures may also promote selective sweeps, niche shifts and ecological speciation during colonization, but these are seldom considered at biogeographical scales. Here we integrate genetic data and Ecologic Niche Models (ENMs) to investigate the historical biogeography and cohesion of the polymorphic rockweed Fucus distichus throughout its immense amphiboreal range, focusing on trans-Arctic asymmetries, glacial/interglacial dynamics, and integrity of sympatric eco-morphotypes. Populations were sampled throughout the Pacific and the Atlantic, from southern rear-edges to the high-Arctic. They were genotyped for seven microsatellites and an mtDNA spacer, and genetic diversity and structure were assessed from global to local scales. ENMs were used to compare niche divergence and magnitude of post-glacial range shifts in Pacific versus Atlantic sub-ranges. Haplotypic and genotypic data revealed distinct and seemingly isolated Pacific vs Arctic/Atlantic gene-pools, with finer-scale regional sub-structuring pervasive in the Pacific. MtDNA diversity was highly structured and overwhelmingly concentrated in the Pacific. Regionally, Alaska showed the highest intra-population diversity but the lowest levels of endemism. Some sympatric/parapatric ecotypes exhibited distinct genotypic/haplotypic compositions. Strikingly, niche models revealed higher Pacific tolerance to maximum temperatures and predicted a much more consolidated presence in the NE Atlantic. Glacial and modern ranges overlapped extensively in the Pacific, whereas the modern Atlantic range was largely glaciated or emerged during the Last Glacial Maximum. Higher genetic and ecogeographic diversity supports a primary Pacific diversification and secondary Atlantic colonization, also likely reflecting the much larger and more stable climatic refugia in the Pacific. The relic distribution and reduced ecological/morphological plasticity in the NE Atlantic are hypothesized to reflect functional trans-Arctic bottlenecks, recent colonization or competition with congeners. Within the Pacific, Alaska showed signatures of a post-glacial melting pot of eastern and southern populations. Genetic/ecotypic variation was generally not sufficiently discontinuous or consistent to justify recognizing multiple taxonomic entities, but support a separate species in the eastern Pacific, at the southern rear-edge. We predict that layered patterns of phylogeographic structure, incipient speciation and niche differences might be common among widespread low-dispersal amphiboreal taxa.
The authors thank Marta Valente (CCMAR), André Silva and Diogo Brito for sequencing and genotyping work and all the people involved in sample collection. Samples from Logy Bay were kindly collected by Kyle R. Millar. DK-J and NM thank Hurtigruten’s FRAM cruise for help with sampling along the Greenland west coast. Greenland sampling was also connected with campaigns for the MarineBasis component of the Greenland Ecosystem Monitoring (GEM) Programme in Nuuk and Young Sound, which is acknowledged.